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• AAExteriorSubstitutionRegister() : bpp::AAExteriorSubstitutionRegister
• aaFitness() : bpp::AbstractCodonAAFitnessSubstitutionModel
• AAInteriorSubstitutionRegister() : bpp::AAInteriorSubstitutionRegister
• aaModel() : bpp::AbstractCodonAARateSubstitutionModel
• abs() : bpp::ExtendedFloat
• AbstractAgglomerativeDistanceMethod() : bpp::AbstractAgglomerativeDistanceMethod
• AbstractAlignedPhyloLikelihood() : bpp::AbstractAlignedPhyloLikelihood
• AbstractAlignedPhyloLikelihoodSet() : bpp::AbstractAlignedPhyloLikelihoodSet
• AbstractAutonomousSubstitutionProcess() : bpp::AbstractAutonomousSubstitutionProcess
• AbstractBiblioMixedTransitionModel() : bpp::AbstractBiblioMixedTransitionModel
• AbstractBiblioSubstitutionModel() : bpp::AbstractBiblioSubstitutionModel
• AbstractBiblioTransitionModel() : bpp::AbstractBiblioTransitionModel
• AbstractCodonAAFitnessSubstitutionModel() : bpp::AbstractCodonAAFitnessSubstitutionModel
• AbstractCodonAARateSubstitutionModel() : bpp::AbstractCodonAARateSubstitutionModel
• AbstractCodonBGCSubstitutionModel() : bpp::AbstractCodonBGCSubstitutionModel
• AbstractCodonClusterAASubstitutionModel() : bpp::AbstractCodonClusterAASubstitutionModel
• AbstractCodonCpGSubstitutionModel() : bpp::AbstractCodonCpGSubstitutionModel
• AbstractCodonDistanceSubstitutionModel() : bpp::AbstractCodonDistanceSubstitutionModel
• AbstractCodonFitnessSubstitutionModel() : bpp::AbstractCodonFitnessSubstitutionModel
• AbstractCodonFrequenciesSubstitutionModel() : bpp::AbstractCodonFrequenciesSubstitutionModel
• AbstractCodonPhaseFrequenciesSubstitutionModel() : bpp::AbstractCodonPhaseFrequenciesSubstitutionModel
• AbstractCodonSubstitutionModel() : bpp::AbstractCodonSubstitutionModel
• AbstractDendrogramPlot() : bpp::AbstractDendrogramPlot
• AbstractDFPSubstitutionModel() : bpp::AbstractDFPSubstitutionModel
• AbstractDiscreteRatesAcrossSitesTreeLikelihood() : bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood
• AbstractFrequencySet() : bpp::AbstractFrequencySet
• AbstractFromSubstitutionModelTransitionModel() : bpp::AbstractFromSubstitutionModelTransitionModel
• AbstractHomogeneousTreeLikelihood() : bpp::AbstractHomogeneousTreeLikelihood
• AbstractIMultiPhyloDAG() : bpp::AbstractIMultiPhyloDAG
• AbstractIMultiPhyloTree() : bpp::AbstractIMultiPhyloTree
• AbstractIMultiTree() : bpp::AbstractIMultiTree
• AbstractIPhyloDAG() : bpp::AbstractIPhyloDAG
• AbstractIPhyloTree() : bpp::AbstractIPhyloTree
• AbstractITree() : bpp::AbstractITree
• AbstractKroneckerCodonSubstitutionModel() : bpp::AbstractKroneckerCodonSubstitutionModel
• AbstractKroneckerWordSubstitutionModel() : bpp::AbstractKroneckerWordSubstitutionModel
• AbstractLkTransitionModel() : bpp::AbstractLkTransitionModel
• AbstractMapping() : bpp::AbstractMapping
• AbstractMixedTransitionModel() : bpp::AbstractMixedTransitionModel
• AbstractMutationProcess() : bpp::AbstractMutationProcess
• AbstractNonHomogeneousTreeLikelihood() : bpp::AbstractNonHomogeneousTreeLikelihood
• AbstractNucleotideSubstitutionModel() : bpp::AbstractNucleotideSubstitutionModel
• AbstractOMultiPhyloDAG() : bpp::AbstractOMultiPhyloDAG
• AbstractOMultiPhyloTree() : bpp::AbstractOMultiPhyloTree
• AbstractOMultiTree() : bpp::AbstractOMultiTree
• AbstractOPhyloDAG() : bpp::AbstractOPhyloDAG
• AbstractOPhyloTree() : bpp::AbstractOPhyloTree
• AbstractOTree() : bpp::AbstractOTree
• AbstractParametrizableSequencePhyloLikelihood() : bpp::AbstractParametrizableSequencePhyloLikelihood
• AbstractPhyloLikelihood() : bpp::AbstractPhyloLikelihood
• AbstractPhyloLikelihoodSet() : bpp::AbstractPhyloLikelihoodSet
• AbstractProteinSubstitutionModel() : bpp::AbstractProteinSubstitutionModel
• AbstractReversibleNucleotideSubstitutionModel() : bpp::AbstractReversibleNucleotideSubstitutionModel
• AbstractReversibleProteinSubstitutionModel() : bpp::AbstractReversibleProteinSubstitutionModel
• AbstractReversibleSubstitutionModel() : bpp::AbstractReversibleSubstitutionModel
• AbstractReward() : bpp::AbstractReward
• AbstractRewardMapping() : bpp::AbstractRewardMapping
• AbstractSequencePhyloLikelihood() : bpp::AbstractSequencePhyloLikelihood
• AbstractSingleDataPhyloLikelihood() : bpp::AbstractSingleDataPhyloLikelihood
• AbstractSinglePhyloSubstitutionMapping() : bpp::AbstractSinglePhyloSubstitutionMapping
• AbstractStateMap() : bpp::AbstractStateMap
• AbstractSubstitutionCount() : bpp::AbstractSubstitutionCount
• AbstractSubstitutionDistance() : bpp::AbstractSubstitutionDistance
• AbstractSubstitutionMapping() : bpp::AbstractSubstitutionMapping
• AbstractSubstitutionModel() : bpp::AbstractSubstitutionModel
• AbstractSubstitutionProcess() : bpp::AbstractSubstitutionProcess
• AbstractSubstitutionRegister() : bpp::AbstractSubstitutionRegister
• AbstractTotallyWrappedSubstitutionModel() : bpp::AbstractTotallyWrappedSubstitutionModel
• AbstractTotallyWrappedTransitionModel() : bpp::AbstractTotallyWrappedTransitionModel
• AbstractTransitionModel() : bpp::AbstractTransitionModel
• AbstractTreeDrawing() : bpp::AbstractTreeDrawing
• AbstractTreeLikelihood() : bpp::AbstractTreeLikelihood
• AbstractTreeLikelihoodData() : bpp::AbstractTreeLikelihoodData
• AbstractTreeParsimonyData() : bpp::AbstractTreeParsimonyData
• AbstractTreeParsimonyScore() : bpp::AbstractTreeParsimonyScore
• AbstractWeightedSubstitutionCount() : bpp::AbstractWeightedSubstitutionCount
• AbstractWordFrequencySet() : bpp::AbstractWordFrequencySet
• AbstractWordSubstitutionModel() : bpp::AbstractWordSubstitutionModel
• AbstractWrappedModel() : bpp::AbstractWrappedModel
• AbstractWrappedSubstitutionModel() : bpp::AbstractWrappedSubstitutionModel
• AbstractWrappedTransitionModel() : bpp::AbstractWrappedTransitionModel
• accessValueConst() : bpp::Value< T >
• accessValueMutable() : bpp::Value< T >
• accessVariableNode() : bpp::AbstractPhyloLikelihood
• addBipartition() : bpp::BipartitionList
• addDistribution() : bpp::SubstitutionProcessCollection
• addEmptyHyperNode() : bpp::MixedSubstitutionModelSet
• addEvent() : bpp::MutationPath
• addFrequencies() : bpp::SubstitutionProcessCollection
• addHyperNode() : bpp::MixedSubstitutionModelSet
• addListener() : bpp::TreeDrawingDisplayControler
• addModel() : bpp::AbstractSinglePhyloSubstitutionMapping , bpp::NonHomogeneousSubstitutionProcess , bpp::SubstitutionModelSet , bpp::SubstitutionProcessCollection , bpp::SubstitutionProcessCollectionMember
• addModelPath() : bpp::ModelScenario
• addNode() : bpp::SiteSimulationResult
• addNsParameter() : bpp::AbstractCodonAAFitnessSubstitutionModel
• addOnePerBranchSubstitutionProcess() : bpp::SubstitutionProcessCollection
• addParametrizable() : bpp::SubstitutionProcessCollection
• addPhyloLikelihood() : bpp::AbstractAlignedPhyloLikelihoodSet , bpp::AbstractPhyloLikelihoodSet , bpp::PhyloLikelihoodContainer , bpp::PhyloLikelihoodSetInterface
• addRateParameter() : bpp::AbstractBiblioTransitionModel , bpp::AbstractFromSubstitutionModelTransitionModel , bpp::AbstractTransitionModel , bpp::BranchModelInterface , bpp::FromMixtureSubstitutionModel , bpp::G2001 , bpp::InMixedSubstitutionModel , bpp::MultinomialFromTransitionModel , bpp::RegisterRatesSubstitutionModel , bpp::TransitionFromTransitionModel , bpp::TS98
• addRegister() : bpp::VectorOfSubstitutionRegisters
• addScenario() : bpp::SubstitutionProcessCollection
• addSon() : bpp::AwareNode , bpp::Node
• addSubstitutionProcess() : bpp::SubstitutionProcessCollection
• addSubstitutionProcessCollectionMember() : bpp::PhylogeneticsApplicationTools
• addSubTree() : bpp::Node , bpp::PhyloTree
• addToHyperNode() : bpp::MixedSubstitutionModelSet
• addToModel() : bpp::MixedSubstitutionModelSet::HyperNode , bpp::ModelPath
• addTopologyListener() : bpp::NNITopologySearch , bpp::TopologySearch
• addTree() : bpp::SubstitutionProcessCollection
• addTreeDrawingListener() : bpp::AbstractTreeDrawing , bpp::TreeDrawing
• addTrivialBipartitions() : bpp::BipartitionList
• addX() : bpp::Cursor
• addY() : bpp::Cursor
• afterDrawBranch() : bpp::BootstrapValuesTreeDrawingListener , bpp::BranchLengthsTreeDrawingListener , bpp::TreeDrawingListener , bpp::TreeDrawingListenerAdapter
• afterDrawNode() : bpp::LabelCollapsedNodesTreeDrawingListener , bpp::LabelInnerNodesTreeDrawingListener , bpp::LeafNamesTreeDrawingListener , bpp::NodesIdTreeDrawingListener , bpp::TreeDrawingListener , bpp::TreeDrawingListenerAdapter
• afterDrawTree() : bpp::TreeDrawingListener , bpp::TreeDrawingListenerAdapter
• AgglomerativeDistanceMethodInterface() : bpp::AgglomerativeDistanceMethodInterface
• aliasParameters() : bpp::SubstitutionProcessCollection
• AlignedLikelihoodCalculation() : bpp::AlignedLikelihoodCalculation
• alignedLikelihoodCalculation() : bpp::AlignedPhyloLikelihoodAutoCorrelation , bpp::AlignedPhyloLikelihoodHmm , bpp::AlignedPhyloLikelihoodInterface , bpp::AlignedPhyloLikelihoodMixture , bpp::AlignedPhyloLikelihoodProduct , bpp::AutoCorrelationProcessPhyloLikelihood , bpp::HmmProcessPhyloLikelihood , bpp::MixtureProcessPhyloLikelihood , bpp::OnABranchPhyloLikelihood , bpp::OneProcessSequencePhyloLikelihood , bpp::PartitionProcessPhyloLikelihood , bpp::SingleProcessPhyloLikelihood
• alignedPhyloLikelihood() : bpp::AbstractAlignedPhyloLikelihoodSet , bpp::AlignedPhyloLikelihoodSetInterface , bpp::HmmPhyloAlphabet
• AlignedPhyloLikelihoodAutoCorrelation() : bpp::AlignedPhyloLikelihoodAutoCorrelation
• AlignedPhyloLikelihoodHmm() : bpp::AlignedPhyloLikelihoodHmm
• AlignedPhyloLikelihoodInterface() : bpp::AlignedPhyloLikelihoodInterface
• AlignedPhyloLikelihoodMixture() : bpp::AlignedPhyloLikelihoodMixture
• AlignedPhyloLikelihoodProduct() : bpp::AlignedPhyloLikelihoodProduct
• allelicAlphabet() : bpp::POMO
• allowWithin() : bpp::CategorySubstitutionRegister
• alphabet() : bpp::AbstractFrequencySet , bpp::AbstractStateMap , bpp::AbstractSubstitutionRegister , bpp::AbstractTransitionModel , bpp::AbstractWrappedModel , bpp::BranchModelInterface , bpp::FrequencySetInterface , bpp::GivenDataSubstitutionProcessSequenceSimulator , bpp::MarkovModulatedSubstitutionModel , bpp::MutationPath , bpp::NonHomogeneousSequenceSimulator , bpp::RegisterRatesSubstitutionModel , bpp::SequenceSimulatorInterface , bpp::SimpleSubstitutionProcessSequenceSimulator , bpp::SimpleSubstitutionProcessSiteSimulator , bpp::SiteSimulationResult , bpp::SiteSimulatorInterface , bpp::StateMapInterface , bpp::SubstitutionModelSet , bpp::SubstitutionProcessSequenceSimulator , bpp::SubstitutionRegisterInterface
• alphabetIndex() : bpp::AbstractReward
• alphabetIndexHasChanged() : bpp::AbstractReward , bpp::DecompositionReward
• AncestralStateReconstruction() : bpp::AncestralStateReconstruction
• AnonymousSubstitutionModel() : bpp::AnonymousSubstitutionModel
• appendModel() : bpp::PairedSiteLikelihoods
• appendModels() : bpp::PairedSiteLikelihoods
• applyParameters() : bpp::AbstractHomogeneousTreeLikelihood , bpp::AbstractNonHomogeneousTreeLikelihood
• areAllCompatible() : bpp::BipartitionList
• areAllCompatibleWith() : bpp::BipartitionList
• areCompatible() : bpp::BipartitionList , bpp::BipartitionTools
• areIdentical() : bpp::BipartitionList , bpp::BipartitionTools
• AutoCorrelationProcessPhyloLikelihood() : bpp::AutoCorrelationProcessPhyloLikelihood
• AutoCorrelationSequenceEvolution() : bpp::AutoCorrelationSequenceEvolution
• AwareNode() : bpp::AwareNode